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| Status |
Public on Oct 06, 2011 |
| Title |
RNA-Seq of human neurons derived from iPS cells Reveals candidate long non-coding RNAs Involved in neurogenesis and neuropsychiatric disorders. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
As a preliminary step towards applying next generation sequencing using neurons derived from patient-specific iPSCs, we have carried out an RNA-Seq analysis on control human neurons. Dramatic changes in the expression of coding genes, long non-coding RNAs (lncRNAs), pseudogenes, and splice isoforms were seen during the transition from pluripotent stem cells to early differentiating neurons. A number of genes that undergo radical changes in expression during this transition include candidates for schizophrenia (SZ), bipolar disorder (BD) and autism spectrum disorders (ASD) that function as transcription factors and chromatin modifiers, such as POU3F2 and ZNF804A, and genes coding for cell adhesion proteins implicated in these conditions including NRXN1 and NLGN1. In addition, a number of novel lncRNAs were found to undergo dramatic changes in expression, one of which is HOTAIRM1, a regulator of several HOXA genes during myelopoiesis. The increase we observed in differentiating neurons suggests a role in neurogenesis as well. Finally, several lncRNAs that map near SNPs associated with SZ in genome wide association studies also increase during neuronal differentiation, suggesting that these novel transcripts may be abnormally regulated in a subgroup of patients.
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| Overall design |
Total RNAs were isolated from both iPS cells and differentiating neurons, and the sequenced material was pre-amplified using the NuGen Ovation amplification system. RNA-Seq libraries were prepared and carried out on Illumina HiSeq200.
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| Contributor(s) |
Lin M, Pedrosa E, Shah A, Hrabovsky A, Maqbool S, Zheng D, Lachman HM |
| Citation(s) |
21915259 |
| Submission date |
Oct 05, 2011 |
| Last update date |
Mar 26, 2021 |
| Contact name |
Mingyan Lin |
| E-mail(s) |
mingyan.lin@phd.einstein.yu.edu
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| Organization name |
Albert Einstein college of medicine
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| Street address |
1300 Morris Park Avenue
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| City |
bronx |
| State/province |
ny |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| SRA |
SRP008681 |
| BioProject |
PRJNA147137 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE32625_RAW.tar |
19.9 Gb |
(http)(custom) |
TAR (of BAM) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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